GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5405 in Caulobacter crescentus NA1000

Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate CCNA_02751 CCNA_02751 ABC transporter ATP-binding protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_5405
         (254 letters)



>FitnessBrowser__Caulo:CCNA_02751
          Length = 332

 Score =  182 bits (463), Expect = 6e-51
 Identities = 103/242 (42%), Positives = 147/242 (60%), Gaps = 5/242 (2%)

Query: 14  IIQMQGVNKWYGQ--FHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRI 71
           +I  Q V+K Y Q     L  ++L+VK GE   + G SG+GKST IR +N LE    G++
Sbjct: 1   MITFQDVSKTYAQGGHPALSGVSLSVKAGEVFGVIGASGAGKSTLIRLINGLETPSAGQV 60

Query: 72  VVDGVELTN-DLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEIA 130
           +VDG ++    +  + A+RR VGM+FQHFNL    T+ QN    P+ +   P  + +   
Sbjct: 61  IVDGDDVAALGVAGLRALRRRVGMIFQHFNLLSGKTVAQNVAF-PLKLAGRPAAEVKART 119

Query: 131 MHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLD 190
              LERV +   A KYP QLSGGQ+QRV IARAL   PK++L DE TSALDPE  +++LD
Sbjct: 120 AELLERVGLSAHAGKYPAQLSGGQKQRVGIARALATNPKVLLCDEATSALDPETTEQILD 179

Query: 191 TMIGL-AEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNDRTKLFL 249
            + GL  E G+T++ +THEM   R V +RV  +D G +VE+ A  + F +P +D  + F+
Sbjct: 180 LIAGLNRELGLTIVLITHEMDVVRRVCDRVAVLDAGRVVEEGAVEEVFLHPASDTARRFV 239

Query: 250 SQ 251
            +
Sbjct: 240 RE 241


Lambda     K      H
   0.322    0.137    0.407 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 187
Number of extensions: 8
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 254
Length of database: 332
Length adjustment: 26
Effective length of query: 228
Effective length of database: 306
Effective search space:    69768
Effective search space used:    69768
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory